Sentinel Site Selection Proposal for Genomic Surveillance in Ethiopia (2020-2024)

Author

Henok T

Introduction

  • Objective: Propose sentinel sites for genomic surveillance in Ethiopia to enhance outbreak detection and response.
  • Data Source: Disease surveillance data (2020-2024) covering 4,852 records from total reporting woredas in the above years.
  • Diseases:
    • Malaria (mal), Meningitis (mng), AFP Polio (afp), Anthrax (anth), Rabies (rab), Measles (msls): 2020-2024.
    • Cholera (chlr): 2022-2024.
    • Dengue Fever (deng_fevr): 2023-2024.
  • Goals:
    • Identify high-burden woredas for each disease.
    • Select woredas with multiple diseases for comprehensive surveillance.
    • Visualize results interactively for stakeholder use.

Methodology: Data Collection and Preparation

  • Scope: Aggregated disease cases by woreda and region from 2020 to 2024.
  • Data Limitations:
    • Cholera data available only from 2022-2024.
    • Dengue fever data available only from 2023-2024.
    • Missing values (NA) treated as zero to ensure consistent analysis.
  • Processing:
    • Summed cases per disease per woreda, respecting data availability periods.
    • Used tidyverse for data cleaning and aggregation.

Methodology: Site Selection Process

  • Step 1: Ranking Woredas per Disease:
    • For each disease, ranked woredas by case count within each region.
    • Selected top 20 woredas for Oromia and Amhara (high-population regions).
    • Selected top 10 woredas for other regions.
  • Step 2: Identifying Multi-Disease Woredas:
    • Identified woredas appearing in multiple disease rankings.
    • Calculated:
      • num_diseases: Number of diseases ranked in top 10/20.
      • diseases_present: List of diseases.
      • total_cases: Sum of cases across all diseases (for context).
    • Filtered for woredas with at least two diseases.
    • Sorted by region, num_diseases (descending), and total_cases (descending).

Methodology: Visualization

  • Tools: Used tmap for interactive mapping and DT for tables(Table isnot working now but will be corrected)
  • Map Components:
    • Woredas colored by num_diseases (Blues palette).
    • Admin 1 (region) boundaries with labels to show geographic context.
    • Popups with details: region, zone, woreda, number of diseases, diseases present, total cases.
  • Table:Interactive display of proposed woredas with filtering and sorting capabilities.
  • Shapefiles:
    • Admin 3 (woredas): eth_admbnda_adm3_csa_bofedb_2021.shp.
    • Admin 1 (regions): eth_admbnda_adm1_csa_bofedb_2021.shp.

Results: Proposed Sentinel Sites - Interactive Table

  • Description:
    • Shows woredas with multiple diseases, proposed as sentinel sites.
    • Columns: region, zone, woreda, num_diseases, diseases_present, total_cases.
  • How to Access and Use:
    • Filter: Use the search bar to find specific regions or woredas.
    • Sort: Click column headers (e.g., num_diseases) to rank by disease count.
    • Navigate: Use pagination to view all entries.
    • Helps stakeholders identify priority woredas for surveillance.

Propose Sentinel Sites - Table

Table is not working, needs maintenance by the creator

Results: Proposed Sentinel Sites - Interactive Table

  • Description:

    • Visualizes proposed sentinel sites (woredas with >=2 diseases).
    • Colored by number of diseasese ( darker blue = more disease reported)
    • Includes Admin 1 boundaries and region names for context.

  • How to use the map:

    • Zoom/Pan: Explore specific regions or woredas.
    • Click:View popups with details (region, zone, woreda, diseases, cases).
    • Legend: Interpret disease count via the color scale.
    • Ideal for spatial analysis and Site prioritization.
    tmap mode set to interactive viewing

Discussion

  • Key Findings:
    • [Placeholder: e.g., “Oromia and Amhara have multiple woredas with 3+ diseases, ideal for surveillance hubs.”]
    • Limited cholera and dengue data may underrepresent some woredas’ burden.
  • Implications:
    • Multi-disease woredas ensure broad pathogen coverage.
  • Limitations:
    • Cholera (2022-2024) and dengue (2023-2024) data gaps.
    • Potential under reporting or missing data (NA values).
    • utilization of cases definitions in healht facilites - hence reported cases might not really be cases.

Conclusion

  • Summary:
    • Proposed sentinel sites based on high disease burden and diversity.
    • Interactive table and map generated to facilitate data-driven decisions.
  • Next Steps:
    • Refine the proposed sites by improving selection approach.
    • Validate sites through discussion with regions and field assessments.
  • Contact: Henok T ([henoktadesse95@gmail.coml])